Intro

introtext

Structural Variants Summary

Below is a series of tables and plots detailing the structural variants identified by NAIBR (publication). The variants are given by:

Name Description
Inversion a segment that broke off and reattached within the same chromosome, but in reverse orientation
Duplication a type of mutation involving the production of one or more copies of a gene or region of a chromosome
Deletion a type of mutation involving the loss of one or more nucleotides from a segment of DNA

This report shows overview information.

In the colorful summary boxes are the per-population average number of variants detected by type.

header info

npops

12

ndeletions

2,330.6

nduplications

6.4

ninversions

15.1

per contig descs

by count

Variants by count

The table below details counts each type of structural variant for every contig for every population.

by length

Variants by length

The table below details the lengths (in bp) of structural variants for every contig for every population.

Per contig counts

Variants by count

Variants by base-pair span

Various Stats

interpreting output

Interpreting Output

NAIBR outputs a tab-delimited file with named columns (along with a VCF and a reformatted bedpe file with extra information). The columns of the bedpe file are deciphered as such:

Column Name Description
Population Name of the population
Chr1 Name of the contig where the variant starts
Break1 Base-pair position in Chr1 of the start of the variant
Chr2 Name of the contig where the variant ends
Break2 Base-pair position in Chr2 of the end of the variant
SplitMolecules Number of split molecules supporting variant
DiscordantReads Number of discordant reads supporting variant
Orientation Orientation of variant relative to reference
Haplotype The haplotype of the variant
Score log-likelihood score for variant
PassFilter PASS if passes internal NAIBR filter threshold, otherwise FAIL
SV The type of variant (inversion, deletion, or duplication)

variants anc chimeras desc

all variants desc

All non-chimeric variants

The table below details the variants detected by NAIBR that appear on a single contig/chromosome and passed the programs internal filtering.

chimeras desc

Chimeric variants

The table below shows any structural variants whose breakpoints span multiple contigs and may require further assessment. These variants are not shown in the plots below.

Variants and Chimeras

all variants

chimeric variants

SV size and location

legend

Visualize the Variants

Below are three circular plots to visualize the distribution of putative structural variants across (up to) 30 of the largest contigs across the groups you specified in your data. If you are unfamiliar with this kind of visualization, it’s a circular version of a linear genome. Each “wedge” is a different contig, from position 0 to the end of the contig, and is labelled by the contig name. Each internal (grey) ring is a plot of observed structural variants for that contig for a different population.

Very small variants may be difficult to see or will not appear on the plot. Deletions are displayed as points as they tend to be small and clump together. You may hover your cursor over variants to view their positions, pan by clicking and dragging, and zoom using scroll (mouse or touchpad). In case you become unable to scroll up from the plot due to these interactive features, place your cursor over the navigation bar of this report and you will be able to scroll the report instead of zooming on the plot.

legendrow

Population legend

plotrow

Inversions

Duplications

Deletions